Methods, challenges, and Promise of

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1、YALEJOURNALOFBIOLOGYANDMEDICINE84(2011),pp.439-446.Copyright©2011.REVIEwMethods,challenges,andPromiseofnext-GenerationSequencingincancerBiologyAdrianD.HaimovichYaleSchoolofMedicine,NewHaven,ConnecticutItisgenerallyacceptedthatcancersresultfromtheaggregationofsomaticmutations.Theemergence

2、ofnext-generationsequencing(NGS†)technologiesduringthepasthalf-decadehasenabledstudiesofcancergenomeswithhighsensitivityandresolutionthroughwhole-genomeandwhole-exomesequencingapproaches,amongothers.Thissaltatoryadvanceintroducesthepossibilityofassemblingmultiplecancergenomesforanalysisi

3、nacost-ef-fectivemanner.Analyticalapproachesarenowappliedtothedetectionofanumberofso-maticgenomealterations,includingnucleotidesubstitutions,insertions/deletions,copynumbervariations,andchromosomalrearrangements.Thisreviewprovidesathoroughin-troductiontothecancergenomicspipelineaswellasa

4、casestudyofthesemethodsputintopractice.IntroductIonneticdeterminantsofhumandiseasecouldOverthecourseofthe10yearsthathavebeelucidatedforarangeofconditionsbasedpassedsincethepublicationofthefirstontheappearanceofuniquegenomicalter-humangenomesequence,thelandscapeofationsingroupsofpatients.

5、cancerresearchhaschangedwithremarkableThefundamentalhypothesisdrivingspeed.Thecompletionofthehumangenomediseasegenomicsisthatthereisaconstel-projectmarkedthebeginningofaneweraoflationofmutationsthatappearinaffectedscientificresearch―oneinwhichthege-persons,butnotinunaffectedpersons.Towho

6、mallcorrespondenceshouldbeaddressed:AdrianD.Haimovich,MD/PhDProgram,YaleSchoolofMedicine,367CedarStreet,ESH316,NewHaven,CT06510:E-mail:adrian.haimovich@yale.edu.†Abbreviations:NGS,next-generationsequencing;SNP,singlenucleotidepolymorphism;SNV,singlenucleotidevariant;PCR,polymerasechainre

7、action;SIFT,SortingIntolerantfromTolerant;KEGG,KyotoEncyclopediaofGenesandGenomes;GO,GeneOntology;GSEA,GeneSetEnhancementAnalysis.Keywords:Cancer,genomics,sequencing,computationThisworkwassupportedbyNIHMSTPTG2T32GM07205.439440Haimovich:GenomeanalysisincancerresearchBasedo